State-of-the-Art Information Retrieval Tools for Biological Resources

2018 ◽  
pp. 77-96
Author(s):  
Shashi Bhushan Lal ◽  
Anu Sharma ◽  
Krishna Kumar Chaturvedi ◽  
Mohammad Samir Farooqi ◽  
Sanjeev Kumar ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Statistical Analysis ◽  
Relevant Information ◽  
Ease Of Use ◽  
Video Data ◽  
Biological Databases ◽  
Biological Resources ◽  
Sequencing Technologies ◽  
Scientific Experiments ◽  
Insight Into

With the advancements in sequencing technologies, there is an exponential growth in the availability of the biological databases. Biological databases consist of information and knowledge collected from scientific experiments, published literature and statistical analysis of text, numerical, image and video data. These databases are widely spread across the globe and are being maintained by many organizations. A number of tools have been developed to retrieve the information from these databases. Most of these tools are available on web but are scattered. So, finding a relevant information is a very difficult, and tedious task for the researchers. Moreover, many of these databases use disparate storage formats but are linked to each other. So, an important issue concerning present biological resources is their availability and integration at single platform. This chapter provides an insight into existing biological resources with an aim to provide consolidated information at one place for ease of use and access by researchers, academicians and students.

State-of-the-Art Information Retrieval Tools for Biological Resources

2017 ◽  
pp. 203-226
Author(s):  
Shashi Bhushan Lal ◽  
Anu Sharma ◽  
Krishna Kumar Chaturvedi ◽  
Mohammad Samir Farooqi ◽  
Sanjeev Kumar ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Statistical Analysis ◽  
Relevant Information ◽  
Ease Of Use ◽  
Video Data ◽  
Biological Databases ◽  
Biological Resources ◽  
Sequencing Technologies ◽  
Scientific Experiments ◽  
Insight Into

With the advancements in sequencing technologies, there is an exponential growth in the availability of the biological databases. Biological databases consist of information and knowledge collected from scientific experiments, published literature and statistical analysis of text, numerical, image and video data. These databases are widely spread across the globe and are being maintained by many organizations. A number of tools have been developed to retrieve the information from these databases. Most of these tools are available on web but are scattered. So, finding a relevant information is a very difficult, and tedious task for the researchers. Moreover, many of these databases use disparate storage formats but are linked to each other. So, an important issue concerning present biological resources is their availability and integration at single platform. This chapter provides an insight into existing biological resources with an aim to provide consolidated information at one place for ease of use and access by researchers, academicians and students.

scholarly journals COVID-19 knowledge graph from semantic integration of biomedical literature and databases

2021 ◽  
Author(s):  
Chuming Chen ◽  
Karen E Ross ◽  
Sachin Gavali ◽  
Julie E Cowart ◽  
Cathy H Wu
Keyword(s):  
Semantic Web ◽  
Relevant Information ◽  
Semantic Integration ◽  
Biomedical Literature ◽  
Knowledge Graph ◽  
Biological Databases ◽  
Global Response ◽  
Semantic Web Technology ◽  
Federated Queries ◽  
Insight Into

Abstract Summary The global response to the COVID-19 pandemic has led to a rapid increase of scientific literature on this deadly disease. Extracting knowledge from biomedical literature and integrating it with relevant information from curated biological databases is essential to gain insight into COVID-19 etiology, diagnosis, and treatment. We used Semantic Web technology RDF to integrate COVID-19 knowledge mined from literature by iTextMine, PubTator, and SemRep with relevant biological databases and formalized the knowledge in a standardized and computable COVID-19 Knowledge Graph (KG). We published the COVID-19 KG via a SPARQL endpoint to support federated queries on the Semantic Web and developed a knowledge portal with browsing and searching interfaces. We also developed a RESTful API to support programmatic access and provided RDF dumps for download. Availability and implementation The COVID-19 Knowledge Graph is publicly available under CC-BY 4.0 license at https://research.bioinformatics.udel.edu/covid19kg/.

scholarly journals Noni fruit’s water spot appearance on the second day of harvest: a trade-off between resistance and energy

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Tian Wu ◽  
Danyan Hu ◽  
Qingfen Wang
Keyword(s):  
Statistical Analysis ◽  
Molecular Level ◽  
Morinda Citrifolia ◽  
Transcriptome Data ◽  
Trade Off ◽  
Kegg Pathways ◽  
Available Energy ◽  
Climacteric Fruit ◽  
The Relationship ◽  
Insight Into

Abstract Background Noni (Morinda citrifolia Linn.) is a tropical tree that bears climacteric fruit. Previous observations and research have shown that the second day (2 d) after harvest is the most important demarcation point when the fruit has the same appearance as the freshly picked fruit (0 d); however, they are beginning to become water spot appearance. We performed a conjoint analysis of metabolome and transcriptome data for noni fruit of 0 d and 2 d to reveal what happened to the fruit at the molecular level. Genes and metabolites were annotated to KEGG pathways and the co-annotated KEGG pathways were used as a statistical analysis. Results We found 25 pathways that were significantly altered at both metabolic and transcriptional levels, including a total of 285 differentially expressed genes (DEGs) and 11 differential metabolites through an integrative analysis of transcriptomics and metabolomics. The energy metabolism and pathways originating from phenylalanine were disturbed the most. The upregulated resistance metabolites and genes implied the increase of resistance and energy consumption in the postharvest noni fruit. Most genes involved in glycolysis were downregulated, further limiting the available energy. This lack of energy led noni fruit to water spot appearance, a prelude to softening. The metabolites and genes related to the resistance and energy interacted and restricted each other to keep noni fruit seemingly hard within two days after harvest, but actually the softening was already unstoppable. Conclusions This study provides a new insight into the relationship between the metabolites and genes of noni fruit, as well as a foundation for further clarification of the post-ripening mechanism in noni fruit.

A distributional semantics-based information retrieval framework for online social networks

2021 ◽  
pp. 1-11
Author(s):  
V.S. Anoop ◽  
P. Deepak ◽  
S. Asharaf
Keyword(s):  
Social Networks ◽  
Information Retrieval ◽  
Online Social Networks ◽  
Latent Dirichlet Allocation ◽  
Relevant Information ◽  
Distributional Semantics ◽  
Scalable Algorithms ◽  
Mobile Platforms ◽  
Cancer Support ◽  
Efficient Extraction

Online social networks are considered to be one of the most disruptive platforms where people communicate with each other on any topic ranging from funny cat videos to cancer support. The widespread diffusion of mobile platforms such as smart-phones causes the number of messages shared in such platforms to grow heavily, thus more intelligent and scalable algorithms are needed for efficient extraction of useful information. This paper proposes a method for retrieving relevant information from social network messages using a distributional semantics-based framework powered by topic modeling. The proposed framework combines the Latent Dirichlet Allocation and distributional representation of phrases (Phrase2Vec) for effective information retrieval from online social networks. Extensive and systematic experiments on messages collected from Twitter (tweets) show this approach outperforms some state-of-the-art approaches in terms of precision and accuracy and better information retrieval is possible using the proposed method.

OP457 A Collaborative Horizon Scanning Alert For Disinvestment And Early Awareness

2020 ◽  
Vol 36 (S1) ◽  
pp. 10-10
Author(s):  
Vigdis Lauvrak ◽  
Kelly Farrah ◽  
Rosmin Esmail ◽  
Anna Lien Espeland ◽  
Elisabet Hafstad ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Interest Group ◽  
Pilot Project ◽  
Relevant Information ◽  
Horizon Scanning ◽  
Google Alerts ◽  
One Year ◽  
The One ◽  
New Research ◽  
Google Search

IntroductionIn 2019, the Norwegian Institute for Public Health and Canadian Agency for Drugs and Technologies in Health (CADTH) received support from HTAi to produce a quarterly current awareness alert for the HTAi Disinvestment and Early Awareness Interest Group in collaboration with the HTAi Information Retrieval Interest Group. The alert focuses on methods and topical issues, and broader forecasts of potentially disruptive technologies that may be of interest to those involved in horizon scanning and disinvestment initiatives in health technology assessment (HTA).MethodsInformation specialists at both agencies developed search strategies for disinvestment and for horizon scanning in PubMed and Google. The template for the alert was based on an e-newsletter developed by the Information Retrieval Interest Group. Information specialists and researchers reviewed the monthly (PubMed) and weekly (Google) search results and selected potentially relevant publications. Additional sources were also identified through regular HTA and horizon scanning work.ResultsAlerts are posted quarterly on the HTAi Interest Group website; members receive an email notice when new alerts are available. While the revised PubMed searches are identifying relevant information, Google alerts have been disappointing, and this search may need to be revised further or dropped. When the one-year pilot project ends, in Fall 2020, interest group members will be surveyed to see if the alerts were useful, and whether they have suggestions for improving them.ConclusionsCollaborating on this alert service reduces duplication of effort between agencies, and makes new research in horizon scanning and disinvestment more accessible to colleagues in other agencies working in these areas.

Open System for Indexing and Retrieving Multimedia Information

2013 ◽  
Author(s):  
Hanene Maghrebi ◽  
Amos David
Keyword(s):  
Information Retrieval ◽  
Multimedia Information ◽  
Open System ◽  
Large Volume ◽  
Retrieval System ◽  
Main Idea ◽  
Relevant Information ◽  
Information Retrieval System ◽  
Multimedia Content ◽  
Nous Proposons

Managing the increasing growth of multimedia content still poses some problems. The challenge is to propose relevant information to the users among the large volume of information available. The main idea that drives our approach is to provide an open information retrieval system, which can adapt its results to several…La gestion de l’information multimédia soulève encore quelques problèmes. Le défi est de pouvoir proposer à l’utilisateur des informations pertinentes parmi la quantité d’information qui ne cesse de s’accroître. Dans cette lignée, nous proposons un système ouvert de recherche d’information capable d’adapter ses résultats aux différents… 

Crowdsourcing the Evaluation of Design Concepts With Empathic Priming

2016 ◽  
Author(s):  
Michelle A. Pang ◽  
Carolyn C. Seepersad
Keyword(s):  
Rating Scales ◽  
Pairwise Comparison ◽  
Comparison Method ◽  
Ease Of Use ◽  
Primary Study ◽  
Design Concepts ◽  
The Impact ◽  
Further Development ◽  
Similar Evaluation ◽  
Insight Into

The evaluation of design concepts is a time consuming and resource intensive process. Crowdsourcing evaluations has been examined in previous work as a means to reduce the need for expert raters, while achieving similar evaluation results. This paper examines the impact of empathically priming novice raters on their evaluation of alternative design concepts. The rating system is based on a pairwise comparison method that requires minimal training of novice raters. In a pilot study the pairwise method for crowdsourcing evaluations is compared with crowdsourced evaluations using non-pairwise rating scales and with the evaluations of expert raters. The primary study incorporates written and empathic priming strategies to determine their impact on novice raters’ evaluation of concepts. Raters are asked to consider several criteria, including novelty, feasibility, clarity (of the concept), usefulness, ease of use, and overall worthiness of further development. Results offer insight into the criteria that are most relevant to novice raters and whether empathic priming has a significant effect on those evaluations.

A Comparison of Three Instructional Approaches in Teaching the Use of the Abridged Readers' Guide to Periodical Literature

1984 ◽  
Vol 12 (3) ◽  
pp. 241-247
Author(s):  
Stephen W. Zsiray
Keyword(s):  
Middle School ◽  
Information Retrieval ◽  
Statistical Analysis ◽  
Instructional Delivery ◽  
Delivery Systems ◽  
Instructional Effectiveness ◽  
Independent Reading ◽  
Periodical Literature ◽  
Library Media ◽  
English Classes

The age of information is upon us and as educators we must teach students how to retrieve information. Three instructional delivery systems were compared for effectiveness in the teaching of library media information retrieval skills. These were: 1) microcomputer-based courseware, 2) lecture, and 3) independent-reading. The eighth grade English classes at the Butler Middle School were randomly selected for placement in one of the above groups. As a result of the study, the statistical analysis indicated that the microcomputer-based courseware was identical in instructional effectiveness to the lecture approach. In addition, both the microcomputer-based and the lecture approach were more effective than the independent-reading method.

Evaluation of changes in mechanical properties of O-ring in one-piece and two-piece ball retained implant-supported overdentures: A three-year retrospective study.

2021 ◽  
Author(s):  
Fathima Banu Raza ◽  
Anand Kumar
Keyword(s):  
Mechanical Properties ◽  
Wear Resistance ◽  
Retrospective Study ◽  
Statistical Analysis ◽  
Wear Rate ◽  
Digital Camera ◽  
Maximum Displacement ◽  
Pin On Disc ◽  
The One ◽  
Insight Into

The o-rings in ball retained overdentures deteriorate with time and need replacement to restore the retentive quality. We evaluated retrospectively the mechanical properties of o-rings after 3 years in function in one and two-piece implant-supported overdentures. The o-rings were retrieved from one-piece (Myriad snap, Equinox-Straumann, 3.3 x 13mm) and two-piece (Neo Biotech, 3.3 x 13mm) implant-supported overdenture patients. A total of 16 pairs of matrices were tested for wear, type of damage and elasticity using Pin on Disc method, USB Digital Camera in 30x zoom and Universal Tensile Machine respectively. The statistical analysis for independent groups were done with the Mann-Whitney U test. Assessment of used O-rings showed 84% more wear in the two-piece system with an abrasive type of damage while 46% wear in the one-piece system with a compressive type of damage. The o-rings in one-piece system showed increase in elongation and maximum displacement to 2% and 7% respectively, while two-piece system showed decrease in elongation and maximum displacement by 13% and 6% respectively. In one-piece system, the loss of retention was more with slow wear rate and in two-piece system, the wear resistance of O-rings decreased due to increased stiffness. Further studies to evaluate the changes in O-ring with increased sample size and at interval 1 year will pave way for insight into the progressive changes in the mechanical properties of an O-ring.

scholarly journals The Value of Abstraction

2019 ◽  
Author(s):  
Mark K Ho ◽  
David Abel ◽  
Tom Griffiths ◽  
Michael L. Littman
Keyword(s):  
Problem Solving ◽  
Relevant Information ◽  
Scaling Up ◽  
Limited Resources ◽  
Abstract Representations ◽  
Learning Research ◽  
Crucial Ingredient ◽  
Insight Into ◽  
Shed Light

Agents that can make better use of computation, experience, time, and memory can solve a greater range of problems more effectively. A crucial ingredient for managing such finite resources is intelligently chosen abstract representations. But, how do abstractions facilitate problem solving under limited resources? What makes an abstraction useful? To answer such questions, we review several trends in recent reinforcement-learning research that provide insight into how abstractions interact with learning and decision making. During learning, abstraction can guide exploration and generalization as well as facilitate efficient tradeoffs---e.g., time spent learning versus the quality of a solution. During computation, good abstractions provide simplified models for computation while also preserving relevant information about decision-theoretic quantities. These features of abstraction are not only key for scaling up artificial problem solving, but can also shed light on what pressures shape the use of abstract representations in humans and other organisms.

Sign in / Sign up

Export Citation Format

Share Document